I found out what the problem was:
The HackRF One used with the Portapack has a shield around the RF part. This shield is exactly opposite to the backup battery.
When looking closely I noticed that the pins that hold the (+) side of the Lithium battery were touching the shield, thus short-circuiting the battery and causing the memory loss.
By bending the pins over the battery, this was fixed and the HackRF One + Portapack are correctly retaining settings and RTC time+date.
I leave this solution for fellow users with the same problem. It is down to the Lithium battery cell holder, which comes with unbended pins.
Regards,
Vitor